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SkillsMP has collected 292 skills from lamm-mit/scienceclaw. Open a skill to review its source and details.
lamm-mit/scienceclawShowing 40 of 292 collected skills.
Retrosynthetic template relevance prediction using a locally deployed ASKCOS TorchServe service. Returns ranked precursor suggestions with confidence scores from 5 template sets (reaxys, pistachio, pistachio_ringbreaker, bkms_metabolic, reaxys_biocatalysis).…
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems…
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
ToolUniverse workflow — Binder Discovery
Computational molecular biology library (sequence I/O, alignment, phylogenetics). Input: FASTA/GenBank/PDB files you already have. Output: parsed sequences, alignments, phylogenetic trees, structural analysis. Does NOT search databases — invoking by topic…
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database…
Search NCBI BLAST for sequence homology and find similar sequences in biological databases
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
Playwright-based browser automation for scraping JavaScript-rendered scientific databases
ToolUniverse workflow — Cancer Variant Interpretation
Rank peptide variants using stability heuristics and hotspot protection; emit top candidates.
Look up chemicals in CAS Common Chemistry (name, CAS RN, SMILES, InChI; ~500k compounds)
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your…
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
Small-molecule drug lookup by exact drug name or ChEMBL ID. Query MUST be a single drug name or ID — 1 to 3 words maximum. Valid examples: 'sotorasib', 'imatinib', 'ibrutinib', 'CHEMBL25', 'AMG 510'. If the topic is 'sotorasib KRAS G12C', the correct query is…
ToolUniverse workflow — Chemical Compound Retrieval
ToolUniverse workflow — Chemical Safety
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use…
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify…
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with…
ToolUniverse workflow — Clinical Guidelines
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates,…
ToolUniverse workflow — Clinical Trial Design
ToolUniverse workflow — Clinical Trial Matching
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Compute per-position conservation/entropy for an aligned peptide MSA (aligned sequences).
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
ToolUniverse workflow — Crispr Screen Analysis
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core…
Transform scientific findings into compelling research narratives for papers, grants, and presentations
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available…
Python cheminformatics library (RDKit wrapper). Input: SMILES strings you already possess. Output: computed molecular properties, fingerprints, conformers, clustering. Does NOT retrieve compounds from any database — querying by topic name returns only a…
Create scientific plots and visualizations using matplotlib and seaborn
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained…
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational…